玉米持绿相关QTL整合图谱构建及一致性QTL区域内候选基因发掘

草业学报 ›› 2012, Vol. 21 ›› Issue (4): 175-185.

玉米持绿相关QTL整合图谱构建及一致性QTL区域内候选基因发掘

方永丰^1,2,3,李永生³,白江平^1,2,3,慕平³,孟亚雄^1,2,3,张金林⁴,王汉宁^1,2,3*,尚勋武^3*

1.甘肃省作物遗传改良与种质创新重点实验室,甘肃兰州 730070;
2.甘肃省干旱生境作物学重点实验室,甘肃兰州 730070;
3.甘肃农业大学农学院,甘肃兰州 730070;
4.兰州大学草地农业科技学院,甘肃兰州 730020

收稿日期:2012-02-20 出版日期:2012-04-25 发布日期:2012-08-20
通讯作者: E-mail:wanghn@gsau.edu.cn,shangxunwu@163.com
作者简介:方永丰(1976-),男,甘肃临洮人,讲师,在读博士。E-mail:fangyf@gsau.edu.cn
基金资助:
973计划前期研究专项(2012CB722902)和甘肃省科技攻关计划项目(2GS064-A41-001-05)资助。

Construction of integration QTL map and identification of candidate genes for stay-green in maize

FANG Yong-feng^1,2,3, LI Yong-sheng³, BAI Jiang-ping^1,2,3, MU Ping³, MENG Ya-xiong^1,2,3, ZHANG Jin-lin⁴, WANG Han-ning^1,2,3, SHANG Xun-wu³

1.Gansu Key Laboratory of Crop Improvement and Germplasm Enhancement, Lanzhou 730070, China;
2.Gansu Provincial Key Laboratory of Aridland Crop Science, Lanzhou 730070, China;
3.College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China;
4. College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China

Received:2012-02-20 Online:2012-04-25 Published:2012-08-20

摘要/Abstract

摘要： 以玉米高密度遗传连锁图谱IBM2 2008 Neighbors为参考图谱,收集来自不同实验中的173个玉米持绿相关数量性状位点(quantitative trait locus,QTL)信息,利用BioMercator 2.1软件,构建出玉米持绿相关QTL整合图谱;采用元分析技术,在1,4,5,9号染色体上发掘出5个持绿“一致性” QTL区间。根据“一致性”QTL区间两端标记在玉米物理图谱B73 RefGen_v2上的位置,将“一致性”QTL区间进行物理图谱定位,利用Plant GDB(http://www.plantgdb.org/)在线区段批量下载工具(download region data)下载“一致性”区间的1 445个预测基因序列并进行生物信息学分析,发现预测基因主要参与具体的细胞过程,执行结合功能,催化、转移酶活性和氧化还原酶活性等分子功能。根据“一致性”QTL区间的基因位点名称,在NCBI中下载相关基因序列,与所在“一致性”QTL区间所有预测基因保守结构域进行比对,在5个“一致性”持绿QTL区间内初步确定8个持绿相关候选基因。利用GRAMENE网站(http://www.gramene.org/)的Cmap功能,将水稻持绿基因sgr(stay green)转定位于玉米物理图谱B73 RefGen_v2上,找到与其同源的玉米候选基因GRMZM2G091837_T01,其序列与已发表的玉米衰老诱导叶绿体持绿蛋白基因sgr1序列一致。

Abstract: Leaf senescence is a character of plant development. Delayed leaf senescence or stay green character has received considerable attention because of its negative impact on photosynthesis and its role in nutrient redistribution within the plant. In the past few decades, a wealth of QTLs (quantitative trait locus) mapping data for stay green and its related traits in maize has been produced using molecular marker approaches. In order to unlock the full potential of the information contained in these independent experiments, 173 stay-green and related QTLs in maize were collected from maize genomic database (maize GDB), and were compiled to construct the integration QTL map for stay-green in maize (Zea mays). The high-scale genetic linkage map of maize IBM2 2008 Neighbors was used as reference and the map were constructed with BioMercator 2.1 software based on the method of meta analysis. Five consensus QTL for maize stay green were identified on maize chromosomes 1, 4, 5 and 9, respectively. After project the consensus QTL region on maize physical map of B73 RefGen_v2, a total of 1 445 candidate genes in the consensus QTL region were discovered and downloaded from Plant GDB(http://www.plantgdb.org/).Meanwhile, according to the results of gene ontology analysis, most candidate genes might take part in the cell development, catalytic process, enzymatic activity and other biological progresses. The sequences of eight stay-green candidate genes were identified by comparatively analyzing the sequences of stay-green gene sequence from other crops. Using a syntonic conservation approach, which is used to comparatively analyze the rice genetic map and maize physical map, one rice gene (sgr) that is coding for the senescence-inducible chloroplast stay-green protein was projected onto the physical map of maize B73RefGen_v2. Therefore, the results suggested that this approach provided an useful tool for identifying QTL conferring stay-green and other candidate genes in maize.

中图分类号:

方永丰,李永生,白江平,慕平,孟亚雄,张金林,王汉宁,尚勋武. 玉米持绿相关QTL整合图谱构建及一致性QTL区域内候选基因发掘[J]. 草业学报, 2012, 21(4): 175-185.

FANG Yong-feng, LI Yong-sheng, BAI Jiang-ping, MU Ping, MENG Ya-xiong, ZHANG Jin-lin, WANG Han-ning, SHANG Xun-wu. Construction of integration QTL map and identification of candidate genes for stay-green in maize[J]. Acta Prataculturae Sinica, 2012, 21(4): 175-185.

参考文献

[1] 乔岩, 王汉宁, 张成, 等. 玉米胚乳突变基因ae连锁累赘的SSR分析[J]. 草业学报, 2011, 20(1): 140-147.
[2] Thomas H, Smart C M. Crops that stay green[J]. Annals of Applied Biology, 1993, 123: 193-219.
[3] Gentinetta E, Ceppi D, Lepori C, et al. A major gene for delayed senescence in maize: Pattern of photosynthates accumulation and inheritance[J]. Plant Breed, 1986, 97: 193-203.
[4] Ma B L, Dwyer L M. Nitrogen uptake and use of two contrasting maize hybrids differing in leaf senescence[J]. Plant and Soil, 1998, 199: 283-291.
[5] Pommel B, Gallais A, Coque M, et al. Carbon and nitrogen allocation and grain filling in three maize hybrids differing in leaf senescence[J]. European Journal of Agronomy, 2006, 24: 203-211.
[6] Bekavac G, Purar B, Stojakovih M, et al. Genetic analysis of stay green trait in broad based maize populations[J]. Cereal Research Communications, 2007, 35(1): 193-203.
[7] 董树亭, 王空军, 胡昌浩, 等. 玉米品种更替过程中群体光合特性的演变[J]. 作物学报, 2000, 26(2): 200-204.
[8] Duvick D N. Genetic rates of grain in hybrid maize yields during the past 40 years[J]. Maydica, 1997, 23: 187-196.
[9] 郑洪建, 沈雪芳, 吴爱忠. 玉米叶片保绿性遗传研究进展[J]. 上海农业学报, 2007, 23(4): 90-94.
[10] Beavis W D, Smith O S, Grant D, et al. Identification of quantitative trait loci using a small sample of top crossed and F4 progeny from maize[J].Crop Science, 1994, 34: 882-896.
[11] Vienne-D, Leonardi-A. Genetics of proteome variation for QTL characterization: application to drought-stress responses in maize[J]. Journal of Experimental Botany, 1999, 50: 303-309.
[12] Zheng H J, Wu A Z, Cai R, et al. QTL mapping of maize (Zea mays L.) stay-green traits and their relationship to yield[J]. Plant Breeding, 2009, 128(1): 54-62.
[13] 王爱玉, 张春庆. 玉米叶绿素含量的QTL定位[J]. 遗传, 2008, 30(8): 1083-1091.
[14] 王春丽. 玉米穗部性状及主要农艺性状发育动态的QTL定位[D]. 郑州: 河南农业大学, 2005.
[15] 刘宗华, 谢惠玲, 王春丽, 等. 氮胁迫和非胁迫条件下玉米不同时期叶绿素含量的QTL分析[J]. 植物营养与肥料学报, 2008, 14(5): 845-851.
[16] 于晓芳. 玉米叶片水分利用效率及其相关性状的QTL 定位与分析[D]. 包头: 内蒙古农业大学, 2010.
[17] 王建康, 李慧慧, 张学才, 等. 中国作物分子设计育种[J]. 作物学报, 2011, 37(2): 191-201.
[18] Goffinet B, Gerber S. Quantitative trait loci: A meta-analysis[J]. Genetics, 2000, 155: 463-473.
[19] Arcade A, Labourdette A, Falque M, et al. BioMercator: integrating genetic maps and QTL towards discovery of candidate genes[J]. Bioinformatics, 2004, 20(14): 2324-2326.
[20] 李立芹, 黄玉碧, 王西瑶. 马铃薯WRKY6基因的克隆、序列分析与原核表达研究[J]. 草业学报, 2011, 20(2): 177-183.
[21] 江腾, 林勇祥, 刘雪, 等. 苜蓿全基因组WRKY转录因子基因的分析[J]. 草业学报, 2011, 20(3): 211-218.
[22] Chardon F, Virlon B, Moreau L, et al. Genetic architecture of flowering time in maize as inferred from quantitative trait loci meta-analysis and synteny conservation with the rice genome[J]. Genetics, 2004, 168: 2169-2185.
[23] Lombard V, Delourme R. A consensus linkage map for rapeseed: Construction and integration of three individual maps from DH populations[J]. Theoretical and Applied Genetics, 2001, 103: 491-507.
[24] Marcel T C, Varshney R K, Barbieri M, et al. A high-density consensus map of barley to compare the distribution of QTLs for partial resistance to Pucciniahordei and of defence gene homologues[J]. Theoretical and Applied Genetics, 2007, 114: 487-500.
[25] 李雪华, 李新海, 郝转芳, 等.干旱条件下玉米耐旱相关性状的QTL一致性图谱构建[J]. 中国农业科学, 2005, 38(5): 882-890.
[26] 栗文娟, 刘志斋, 石云素, 等. 基于元分析和生物信息学分析的玉米抗旱相关性状QTL 一致性区间定位[J].作物学报, 2010, 36(9): 1457-1467.
[27] 王毅, 姚骥,张征锋, 等. 基于玉米综合QTL图谱的比较分析及株高QTL的统合分析[J]. 科学通报, 2006, 51(15): 1776-1786.
[28] 张耿, 祝丽英, 陈景堂, 等. 玉米产量相关性状QTL通用图谱的构建及功能候选基因的开发[J]. 华北农学报, 2008, 23(6): 22-27.
[29] 王帮太, 吴建宇, 丁俊强, 等. 玉米产量及产量相关性状QTL的图谱整合[J]. 作物学报, 2009, 35(10): 1836-1843.
[30] 王晓丽, 李新海, 王振华, 等. 玉米产量因子QTL 整合图谱构建与“一致性”QTL 确定[J]. 核农学报, 2008, 22(6): 756-761.
[31] 吉海莲, 李新海, 谢传晓, 等. 基于元分析的抗玉米丝黑穗病QTL比较定位[J]. 植物遗传资源学报, 2007, 8(2): 132-139.
[32] Darvasi A, Soller M. A simple method to calculate resolving power and confidence interval of QTL map location[J]. Behavior Genetices, 1997, 27: 125-132.
[33] Ashbumer M. Gene ontology: tool for the unifieation of biology.The Gene Ontology Consortium[J]. Nature Genet, 2000, 25(1): 25-29.
[34] Tuberosa R, Salvi S, Sanguineti M, et al. Mapping QTL regulating morphophysiological traits and yield: Casestudies, short comings and perspectives in drought stressed maize[J]. Annales Botabici Fennici, 2002, 89(7): 941-963.
[35] 严建兵, 汤华, 黄益勤, 等. 玉米和水稻重要性状QTL的比较研究[J].遗传学报, 2004, 31: 1401-1407.
[36] Alexandrov N N, Brover W, Freidin S, et al. Insight into corn genes derived from large scale cDNA sequencing[J]. Plant Molecular Biology, 2009, 69: 179-194.
[37] Carol S, Anne D, Dave K, et al. Sequencing, mapping, and analysis of 27, 455 maize full-length cDNAs[J].Plos Genetics, 2009, 5(11): 1000713-1000741.
[38] Wong J C, Lambert R J, Wurt zel E T, et al. QTL and candidate genes phytoenesynthase and zetacarotene desaturase associated with the accumulation of carotenoids in maize[J]. Theoretical and Applied Genetics, 2004, 108(2): 349-359.
[39] Zhang P, Wang Y, Zhang J, et al. A maize QTL for silk maysin levels contains duplicated Myb-homologous genes which jointly regulate flavone biosynthesis[J]. Plant Molecular Biology, 2003, 52(1): 1-15.
[40] 肖景华, 吴昌银, 韩斌, 等. 中国水稻功能基因组研究进展[J]. 中国科学C辑: 生命科学, 2009, 39(10): 909-924.